CPZ

carboxypeptidase Z, the group of M14 carboxypeptidases

Basic information

Region (hg38): 4:8592660-8619759

Links

ENSG00000109625 ∙ NCBI:8532 ∙ OMIM:603105 ∙ HGNC:2333 ∙ Uniprot:Q66K79 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPZ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPZ gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	14	20
missense			85	8	10	103
nonsense			2	1		3
start loss			1			1
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region				2	4	6
non coding			2	2	5	9
Total	0	0	92	17	29

Variants in CPZ

This is a list of pathogenic ClinVar variants found in the CPZ region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-8592824-C-T		CPZ-related disorder	Likely benign (Jan 02, 2020)
4-8592844-C-A		not specified	Uncertain significance (Dec 16, 2021)
4-8592845-G-C		CPZ-related disorder	Benign (Dec 13, 2019)
4-8592850-C-T		CPZ-related disorder	Benign (Nov 19, 2019)
4-8592855-C-A		not specified	Uncertain significance (Apr 04, 2024)
4-8592869-C-T			Likely benign (Apr 01, 2023)
4-8592876-G-A		not specified	Uncertain significance (Feb 28, 2023)
4-8592889-G-C		CPZ-related disorder	Benign (Nov 25, 2019)
4-8592901-A-G		not specified	Uncertain significance (Feb 28, 2023)
4-8592914-C-A		not specified	Uncertain significance (Mar 20, 2024)
4-8599461-C-T		not specified	Uncertain significance (Feb 17, 2024)
4-8599471-C-T		not specified	Uncertain significance (Nov 09, 2021)
4-8601164-G-T		not specified	Uncertain significance (Oct 06, 2024)
4-8601173-C-A		not specified	Uncertain significance (Jan 27, 2022)
4-8601184-C-A		not specified	Uncertain significance (Feb 22, 2023)
4-8601203-C-T		not specified	Uncertain significance (Dec 14, 2022)
4-8601204-G-A		not specified	Uncertain significance (Jun 05, 2024)
4-8601207-C-T		not specified	Uncertain significance (Jan 08, 2024)
4-8601232-C-T		CPZ-related disorder	Benign (Nov 26, 2019)
4-8601260-C-A		not specified	Uncertain significance (Mar 19, 2024)
4-8601289-C-G		not specified	Uncertain significance (Mar 01, 2023)
4-8601318-C-T		not specified	Uncertain significance (Oct 06, 2022)
4-8601332-G-A		not specified	Uncertain significance (Jul 26, 2024)
4-8601341-G-A		not specified	Uncertain significance (Nov 07, 2024)
4-8601342-T-C		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPZ	protein_coding	protein_coding	ENST00000360986	11	27102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.81e-36	7.61e-9	125030	0	717	125747	0.00285

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.43	675	420	1.61	0.0000282	4151
Missense in Polyphen		283	176.33	1.6049		1740
Synonymous	-6.68	293	179	1.64	0.0000128	1292
Loss of Function	-3.26	43	25.3	1.70	0.00000117	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00473	0.00472
Ashkenazi Jewish	0.00562	0.00557
East Asian	0.00595	0.00572
Finnish	0.00347	0.00347
European (Non-Finnish)	0.00217	0.00216
Middle Eastern	0.00595	0.00572
South Asian	0.00259	0.00252
Other	0.00362	0.00359

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves substrates with C-terminal arginine residues. Probably modulates the Wnt signaling pathway, by cleaving some undefined protein. May play a role in cleavage during prohormone processing. {ECO:0000269|PubMed:11766880, ECO:0000269|PubMed:12417617, ECO:0000269|PubMed:9099699}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• rvis_EVS: -1.49
• rvis_percentile_EVS: 3.62

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.197
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cpz

Gene ontology

• Biological process: proteolysis;peptide metabolic process;Wnt signaling pathway;protein processing
• Cellular component: extracellular space
• Molecular function: metallocarboxypeptidase activity;zinc ion binding